Debian Med Project
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Summary
Cloud
Debian Med bioinformatics applications usable in cloud computing

This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited.

Translate description

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks
Index of all tasks

Debian Med Cloud packages

Official Debian packages with high relevance

abyss
??? missing short description for package abyss :-(
Versions of package abyss
ReleaseVersionArchitectures
bookworm2.3.5+dfsg-2amd64,arm64,mips64el,ppc64el,s390x
bullseye2.2.5+dfsg-1amd64,arm64,armhf,i386
sid2.3.10-2amd64,arm64,loong64,ppc64el,riscv64,s390x
forky2.3.10-2amd64,arm64,ppc64el,riscv64,s390x
trixie2.3.10-1amd64,arm64,ppc64el,riscv64,s390x
Debtags of package abyss:
roleprogram
Popcon: 7 users (33 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Shaun D. Jackman, Benjamin P. Vandervalk, Hamid Mohamadi, Justin Chu, Sarah Yeo, S. Austin Hammond, Golnaz Jahesh, Hamza Khan, Lauren Coombe, Rene L. Warren and İnanç Birol: "ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter". (PubMed,eprint) Genome Research 27(5):768-777 (2017)
Registry entries: Bio.tools  SciCrunch  Bioconda 
Topics: Sequence assembly
acedb-other
??? missing short description for package acedb-other :-(
Versions of package acedb-other
ReleaseVersionArchitectures
bookworm4.9.39+dfsg.02-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye4.9.39+dfsg.02-5amd64,arm64,armhf,i386
sid4.9.39+dfsg.02-9amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
Debtags of package acedb-other:
biologynuceleic-acids
fieldbiology, biology:bioinformatics
roleprogram
scopeutility
Popcon: 1 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: L. D. Stein and J. Thierry-Mieg: AceDB: a genome database management system. Computing in Science and Engineering 1(3):44-52 (1999)
Registry entries: Bio.tools 
aevol
??? missing short description for package aevol :-(
Versions of package aevol
ReleaseVersionArchitectures
bookworm5.0+ds-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye5.0+ds-2amd64,arm64,armhf,i386
sid9.3.0-1amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie5.0+ds-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
upstream9.4.0
Popcon: 8 users (30 upd.)*
Newer upstream!
 License: DFSG free
Git
alien-hunter
??? missing short description for package alien-hunter :-(
Versions of package alien-hunter
ReleaseVersionArchitectures
forky1.7-10all
bullseye1.7-8all
bookworm1.7-10all
trixie1.7-10all
sid1.7-10all
Debtags of package alien-hunter:
fieldbiology, biology:structural
roleprogram
scopeutility
useanalysing
Popcon: 6 users (31 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Georgios S. Vernikos and Julian Parkhill: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. (PubMed,eprint) Bioinformatics 22(18):2196-2203 (2006)
Registry entries: SciCrunch 
altree
??? missing short description for package altree :-(
Versions of package altree
ReleaseVersionArchitectures
bookworm1.3.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.3.1-10amd64,arm64,armhf,i386
sid1.3.2-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky1.3.2-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie1.3.2-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Debtags of package altree:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram, shared-lib
scopeutility
useanalysing, comparing
works-with-formatplaintext
Popcon: 6 users (31 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Claire Bardel, Vincent Danjean and Emmanuelle Genin: ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees. (PubMed,eprint) Bioinformatics 22(11):1402-1403 (2006)
Registry entries: SciCrunch 
amap-align
??? missing short description for package amap-align :-(
Versions of package amap-align
ReleaseVersionArchitectures
forky2.2+git20080214.600fc29+dfsg-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye2.2+git20080214.600fc29+dfsg-2amd64,arm64,armhf,i386
bookworm2.2+git20080214.600fc29+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.2+git20080214.600fc29+dfsg-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid2.2+git20080214.600fc29+dfsg-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package amap-align:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
useanalysing, comparing
works-with-formatplaintext
Popcon: 12 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Ariel S. Schwartz and Lior Pachter: Multiple alignment by sequence annealing. (eprint) Bioinformatics 23(2):e24-e29 (2007)
Registry entries: SciCrunch  Bioconda 
ampliconnoise
??? missing short description for package ampliconnoise :-(
Versions of package ampliconnoise
ReleaseVersionArchitectures
sid1.29-17amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie1.29-15amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye1.29-9amd64,arm64,armhf,i386
bookworm1.29-10amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky1.29-17amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
Debtags of package ampliconnoise:
roleprogram
Popcon: 10 users (32 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh: Removing Noise From Pyrosequenced Amplicons. (PubMed,eprint) BMC Bioinformatics 12:38 (2011)
Registry entries: Bio.tools  SciCrunch 
Topics: Sequencing
anfo
??? missing short description for package anfo :-(
Versions of package anfo
ReleaseVersionArchitectures
bullseye0.98-8amd64,arm64,armhf,i386
Popcon: 1 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
Registry entries: SciCrunch 
Topics: Sequencing
aragorn
??? missing short description for package aragorn :-(
Versions of package aragorn
ReleaseVersionArchitectures
forky1.2.41-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie1.2.41-3amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm1.2.38-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.2.38-4amd64,arm64,armhf,i386
sid1.2.41-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Popcon: 7 users (32 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Dean Laslett and Bjorn Canback: ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. (PubMed,eprint) Nucleic Acids Research 32(1):11-16 (2004)
Registry entries: SciCrunch  Bioconda 
Topics: Functional, regulatory and non-coding RNA
arden
??? missing short description for package arden :-(
Versions of package arden
ReleaseVersionArchitectures
forky1.0-6all
bookworm1.0-5all
bullseye1.0-5all
sid1.0-6all
trixie1.0-6all
Popcon: 6 users (32 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Sven H. Giese, Franziska Zickmann and Bernhard Y. Renard: Specificity control for read alignments using an artificial reference genome-guided false discovery rate. (PubMed,eprint) Bioinformatics 30(1):9-16 (2013)
Registry entries: SciCrunch 
Topics: Sequencing
autodock
??? missing short description for package autodock :-(
Versions of package autodock
ReleaseVersionArchitectures
sid4.2.6-9amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm4.2.6-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie4.2.6-9amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky4.2.6-9amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye4.2.6-8amd64,arm64,armhf,i386
Debtags of package autodock:
fieldbiology, biology:structural
interfacecommandline
roleprogram
scopeutility
useanalysing
works-with3dmodel
Popcon: 8 users (33 upd.)*
Versions and Archs
 License: DFSG free
Git
The package is enhanced by the following packages: autogrid
Screenshots of package autodock
autodock-vina
??? missing short description for package autodock-vina :-(
Versions of package autodock-vina
ReleaseVersionArchitectures
trixie1.2.7-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid1.2.7-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye1.1.2-6amd64,arm64,armhf,i386
bookworm1.2.3-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky1.2.7-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Popcon: 9 users (35 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Oleg Trott and Arthur J. Olson: AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. (eprint) Journal of Computational Chemistry 31(2):455-461 (2010)
Registry entries: Bio.tools  SciCrunch  Bioconda 
autogrid
??? missing short description for package autogrid :-(
Versions of package autogrid
ReleaseVersionArchitectures
bookworm4.2.6-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid4.2.6-9amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky4.2.6-9amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye4.2.6-8amd64,arm64,armhf,i386
trixie4.2.6-9amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Debtags of package autogrid:
fieldbiology, biology:structural
interfacecommandline
roleprogram
scopeutility
useanalysing
works-with3dmodel
Popcon: 7 users (32 upd.)*
Versions and Archs
 License: DFSG free
Git
bamtools
??? missing short description for package bamtools :-(
Versions of package bamtools
ReleaseVersionArchitectures
bookworm2.5.2+dfsg-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.5.3+dfsg-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky2.5.3+dfsg-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie2.5.2+dfsg-6amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye2.5.1+dfsg-9amd64,arm64,armhf,i386
Popcon: 10 users (43 upd.)*
Versions and Archs
 License: DFSG free
Git
The package is enhanced by the following packages: multiqc
Please cite: Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael P. Stromberg and Gabor T. Marth: BamTools: a C++ API and toolkit for analyzing and managing BAM files. (PubMed,eprint) Bioinformatics 27(12):1691-2 (2011)
Registry entries: Bio.tools  SciCrunch  Bioconda 
bedtools
??? missing short description for package bedtools :-(
Versions of package bedtools
ReleaseVersionArchitectures
bookworm2.30.0+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.31.1+dfsg-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye2.30.0+dfsg-1amd64,arm64,armhf,i386
forky2.31.1+dfsg-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie2.31.1+dfsg-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Debtags of package bedtools:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopesuite
useanalysing, comparing, converting, filtering
works-withbiological-sequence
Popcon: 60 users (111 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Aaron R. Quinlan and Ira M. Hall: BEDTools: a flexible suite of utilities for comparing genomic features. (PubMed,eprint) Bioinformatics 26(6):841-842 (2010)
Registry entries: Bio.tools  SciCrunch  Bioconda 
bioperl
??? missing short description for package bioperl :-(
Versions of package bioperl
ReleaseVersionArchitectures
bookworm1.7.8-1all
bullseye1.7.7-2all
trixie1.7.8-1all
sid1.7.8-3all
forky1.7.8-3all
Debtags of package bioperl:
devellang:perl, library
fieldbiology, biology:bioinformatics
roledevel-lib, shared-lib
Popcon: 20 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G R Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehvaslaiho, Chad Matsalla, Chris J Mungall, Brian I Osborne, Matthew R Pocock, Peter Schattner, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson and Ewan Birney: The Bioperl toolkit: Perl modules for the life sciences. (PubMed,eprint) Genome Res. 12(10):1611-1618 (2002)
Registry entries: Bio.tools  SciCrunch  Bioconda 
bioperl-run
??? missing short description for package bioperl-run :-(
Versions of package bioperl-run
ReleaseVersionArchitectures
bookworm1.7.3-9all
trixie1.7.3-13all
sid1.7.3-14all
bullseye1.7.3-6all
Debtags of package bioperl-run:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
Popcon: 6 users (35 upd.)*
Versions and Archs
 License: DFSG free
Git
The package is enhanced by the following packages: clustalw exonerate kalign mcl
biosquid
??? missing short description for package biosquid :-(
Versions of package biosquid
ReleaseVersionArchitectures
trixie1.9g+cvs20050121-15.1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye1.9g+cvs20050121-12amd64,arm64,armhf,i386
bookworm1.9g+cvs20050121-12amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky1.9g+cvs20050121-16amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid1.9g+cvs20050121-16amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package biosquid:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
usecomparing, converting, editing
Popcon: 8 users (40 upd.)*
Versions and Archs
 License: DFSG free
Git
bowtie
??? missing short description for package bowtie :-(
Versions of package bowtie
ReleaseVersionArchitectures
forky1.3.1-3amd64,arm64,loong64,ppc64el,riscv64,s390x
bullseye1.3.0+dfsg1-1amd64,arm64
bookworm1.3.1-1amd64,arm64,mips64el,ppc64el,s390x
sid1.3.1-3amd64,arm64,loong64,ppc64el,riscv64,s390x
trixie1.3.1-3amd64,arm64,ppc64el,riscv64,s390x
Debtags of package bowtie:
biologynuceleic-acids
fieldbiology:bioinformatics
interfacecommandline
roleprogram
sciencecalculation
scopeutility
useanalysing, comparing
works-withbiological-sequence
Popcon: 20 users (35 upd.)*
Versions and Archs
 License: DFSG free
Git
The package is enhanced by the following packages: bowtie-examples multiqc
Please cite: Ben Langmead, Cole Trapnell, Mihai Pop and Steven L Salzberg: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. (eprint) Genome Biology 10:R25 (2009)
Registry entries: Bio.tools  SciCrunch  Bioconda 
Topics: Genomics
bowtie2
??? missing short description for package bowtie2 :-(
Versions of package bowtie2
ReleaseVersionArchitectures
forky2.5.5-1amd64,arm64,loong64,ppc64el,riscv64
bullseye2.4.2-2amd64,arm64
bookworm2.5.0-3amd64,arm64,mips64el,ppc64el
trixie2.5.4-1amd64,arm64,ppc64el,riscv64
sid2.5.5-1amd64,arm64,loong64,ppc64el,riscv64
Popcon: 24 users (40 upd.)*
Versions and Archs
 License: DFSG free
Git
The package is enhanced by the following packages: bowtie2-examples multiqc
Please cite: Ben Langmead and Steven L Salzberg: Fast gapped-read alignment with Bowtie 2. (PubMed) Nature Methods 9:357–359 (2012)
Registry entries: Bio.tools  SciCrunch  Bioconda 
Topics: Genomics
boxshade
??? missing short description for package boxshade :-(
Versions of package boxshade
ReleaseVersionArchitectures
sid3.3.1-14amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky3.3.1-14amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm3.3.1-14amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie3.3.1-14amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye3.3.1-14amd64,arm64,armhf,i386
Debtags of package boxshade:
biologyformat:aln, nuceleic-acids, peptidic
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
usetypesetting
works-with-formathtml, plaintext, postscript, tex
Popcon: 11 users (30 upd.)*
Versions and Archs
 License: DFSG free
Git
Registry entries: Bio.tools  SciCrunch 
bwa
??? missing short description for package bwa :-(
Versions of package bwa
ReleaseVersionArchitectures
forky0.7.19-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm0.7.17-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye0.7.17-6amd64,arm64,armhf,i386
trixie0.7.18-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid0.7.19-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package bwa:
biologynuceleic-acids, peptidic
fieldbiology, biology:bioinformatics
interfacecommandline, text-mode
roleprogram
useanalysing, comparing
Popcon: 19 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Heng Li and Richard Durbin: Fast and accurate short read alignment with Burrows-Wheeler transform. (PubMed,eprint) Bioinformatics 25(14):1754-1760 (2009)
Registry entries: Bio.tools  SciCrunch  Bioconda 
cassiopee
??? missing short description for package cassiopee :-(
Versions of package cassiopee
ReleaseVersionArchitectures
trixie1.0.9-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid1.0.9-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky1.0.9-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm1.0.9-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.0.9-3amd64,arm64,armhf,i386
Popcon: 6 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
Registry entries: SciCrunch  Bioconda 
cd-hit
??? missing short description for package cd-hit :-(
Versions of package cd-hit
ReleaseVersionArchitectures
bookworm4.8.1-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid4.8.1-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky4.8.1-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye4.8.1-3amd64,arm64,armhf,i386
trixie4.8.1-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Popcon: 10 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Weizhong Li and Adam Godzik: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.. (PubMed,eprint) Bioinformatics 22 (2006)
Registry entries: Bio.tools  SciCrunch  Bioconda 
Topics: Genomics
cdbfasta
??? missing short description for package cdbfasta :-(
Versions of package cdbfasta
ReleaseVersionArchitectures
sid1.00+git20230710.da8f5ba+dfsg-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky1.00+git20230710.da8f5ba+dfsg-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie1.00+git20230710.da8f5ba+dfsg-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm1.00+git20181005.014498c+dfsg-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.00+git20181005.014498c+dfsg-2amd64,arm64,armhf,i386
Popcon: 10 users (35 upd.)*
Versions and Archs
 License: DFSG free
Git
Registry entries: SciCrunch 
circos
??? missing short description for package circos :-(
Versions of package circos
ReleaseVersionArchitectures
forky0.69.9+dfsg-3all
bullseye0.69.9+dfsg-2all
bookworm0.69.9+dfsg-2all
trixie0.69.9+dfsg-2all
sid0.69.9+dfsg-3all
Debtags of package circos:
fieldbiology:bioinformatics
roleprogram
useviewing
Popcon: 6 users (33 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Martin I Krzywinski, Jacqueline E Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones and Marco A Marra: Circos: An information aesthetic for comparative genomics. (PubMed,eprint) Genome Research 19(9):1639-45 (2009)
Registry entries: Bio.tools  SciCrunch  Bioconda 
clearcut
??? missing short description for package clearcut :-(
Versions of package clearcut
ReleaseVersionArchitectures
sid1.0.9+git20211013.b799afe-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky1.0.9+git20211013.b799afe-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye1.0.9-6amd64,arm64,armhf,i386
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Please cite: Jason Evans, Luke Sheneman and James A. Foster: Relaxed Neighbor-Joining: A Fast Distance-Based Phylogenetic Tree Construction Method. (PubMed) J. Mol. Evol. 62(6):785-792 (2006)
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clonalframe
??? missing short description for package clonalframe :-(
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Please cite: Xavier Didelot and Daniel Falush: Inference of Bacterial Microevolution Using Multilocus Sequence Data. (PubMed,eprint) Genetics Advance 175:1251-1266 (2006)
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clustalo
??? missing short description for package clustalo :-(
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Please cite: Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson and Desmond G Higgins: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. (PubMed,eprint) Molecular Systems Biology 7:539 (2011)
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Topics: Sequence analysis
clustalw
??? missing short description for package clustalw :-(
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Please cite: M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson and D. G. Higgins: Clustal W and Clustal X version 2.0. (PubMed,eprint) Bioinformatics 23(21):2947-2948 (2007)
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Topics: Sequence analysis
concavity
??? missing short description for package concavity :-(
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The package is enhanced by the following packages: conservation-code
Please cite: John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh and Thomas A. Funkhouser: Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. (PubMed) PLoS Computational Biology 5(12):e1000585 (2009)
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conservation-code
??? missing short description for package conservation-code :-(
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Please cite: John A. Capra and Mona Singh: Predicting functionally important residues from sequence conservation. (PubMed) Bioinformatics 23(15):1875-82 (2007)
datamash
??? missing short description for package datamash :-(
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dialign
??? missing short description for package dialign :-(
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Please cite: Burkhard Morgenstern: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. (PubMed,eprint) Bioinformatics 15(3):211-218 (1999)
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dialign-tx
??? missing short description for package dialign-tx :-(
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The package is enhanced by the following packages: dialign-tx-data
Please cite: Amarendran R. Subramanian, Michael Kaufmann and Burkhard Morgenstern: DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. (PubMed) Algorithms for Molecular Biology 3(1):6 (2008)
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discosnp
??? missing short description for package discosnp :-(
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disulfinder
??? missing short description for package disulfinder :-(
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Please cite: Alessio Ceroni, Andrea Passerini, Alessandro Vullo and Paolo Frasconi: DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. (PubMed) Nucleic Acids Res 34(Web Server issue):W177-181 (2006)
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dnaclust
??? missing short description for package dnaclust :-(
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Please cite: Mohammadreza Ghodsi, Bo Liu and Mihai Pop: DNACLUST: accurate and efficient clustering of phylogenetic marker genes. (PubMed,eprint) BMC Bioinformatics 12:271 (2011)
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dssp
??? missing short description for package dssp :-(
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Please cite: W. Kabsch and C. Sander: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.. (PubMed) Biopolymers 22:2577-2637 (1983)
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embassy-domainatrix
??? missing short description for package embassy-domainatrix :-(
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embassy-domalign
??? missing short description for package embassy-domalign :-(
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embassy-domsearch
??? missing short description for package embassy-domsearch :-(
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emboss
??? missing short description for package emboss :-(
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The package is enhanced by the following packages: clustalw primer3
Please cite: Peter Rice, Ian Longden and Alan Bleasby: EMBOSS: The European Molecular Biology Open Software Suite. (PubMed) Trends in Genetics 16(6):276 - 277 (2000)
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exonerate
??? missing short description for package exonerate :-(
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Please cite: Guy C. Slater and Ewan Birney: Automated generation of heuristics for biological sequence comparison. (PubMed,eprint) BMC Bioinformatics 6(1):31 (2005)
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fastdnaml
??? missing short description for package fastdnaml :-(
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Please cite: Gary J. Olsen, Hideo Matsuda, Ray Hagstrom and Ross Overbeek: fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. (PubMed,eprint) Comput Appl Biosci 10(1):41-48 (1994)
fastlink
??? missing short description for package fastlink :-(
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Please cite: R. W. Cottingham Jr., R. M. Idury and A. A. Schaffer: Faster Sequential Genetic Linkage Computations. (PubMed,eprint) American Journal of Human Genetics 53(1):252-263 (1993)
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fastqc
??? missing short description for package fastqc :-(
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The package is enhanced by the following packages: multiqc
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Topics: Sequencing
fasttree
??? missing short description for package fasttree :-(
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Please cite: Morgan N. Price, Paramvir S. Dehal and Adam P. Arkin: FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments.. (PubMed,eprint) PLoS ONE 5(3):e9490 (2010)
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fitgcp
??? missing short description for package fitgcp :-(
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Please cite: Martin S. Lindner, Maximilian Kollock, Franziska Zickmann and Bernhard Y. Renard: Analyzing genome coverage profiles with applications to quality control in metagenomics. (PubMed,eprint) Bioinformatics 29(10):1260-1267 (2013)
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flexbar
??? missing short description for package flexbar :-(
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The package is enhanced by the following packages: multiqc
Please cite: Matthias Dodt, Johannes T. Roehr, Rina Ahmed and Christoph Dieterich: FLEXBAR — Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. (eprint) Biology 1(3):895-905 (2012)
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freecontact
??? missing short description for package freecontact :-(
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Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics (2014)
Topics: Structure prediction; Sequence analysis
gasic
??? missing short description for package gasic :-(
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The package is enhanced by the following packages: gasic-examples
Please cite: Martin S. Lindner and Bernhard Y. Renard: Metagenomic abundance estimation and diagnostic testing on species level. (PubMed,eprint) Nucleic Acids Research 41(1):e10 (2013)
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genometools
??? missing short description for package genometools :-(
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Please cite: Gordon Gremme, Sascha Steinbiss and Stefan Kurtz: GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.. (PubMed) IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(3):645-656 (2013)
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gff2aplot
??? missing short description for package gff2aplot :-(
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Please cite: J. F. Abril, R. Guigó and T. Wiehe: gff2aplot: Plotting sequence comparisons. (PubMed,eprint) Bioinformatics 19(18):2477-2479 (2003)
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gff2ps
??? missing short description for package gff2ps :-(
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Please cite: J. F. Abril and R. Guigó: gff2ps: visualizing genomic annotations.. (PubMed,eprint) Bioinformatics 16(8):743-744 (2000)
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glam2
??? missing short description for package glam2 :-(
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Please cite: Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe and Timothy L. Bailey: Discovering Sequence Motifs with Arbitrary Insertions and Deletions. (PubMed) PLoS Computational Biology 4(5):e1000071 (2008)
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gmap
??? missing short description for package gmap :-(
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Please cite: Thomas D. Wu and Serban Nacu: Fast and SNP-tolerant detection of complex variants and splicing in short reads. (PubMed,eprint) Bioinformatics 26(7):873-81 (2010)
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grinder
??? missing short description for package grinder :-(
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Please cite: Florent E. Angly, Dana Willner, Forest Rohwer, Philip Hugenholtz and Gene W. Tyson: Grinder: a versatile amplicon and shotgun sequence simulator. (PubMed,eprint) Nucleic Acids Research Epub ahead of print (2012)
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gromacs
??? missing short description for package gromacs :-(
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Please cite: Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. (eprint) J. Chem. Theory Comput. 4(3):435-447 (2008)
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hhsuite
??? missing short description for package hhsuite :-(
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Please cite: Michael Remmert, Andreas Biegert, Andreas Hauser and Johannes Söding: HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.. (PubMed) Nat. Methods 9(2):173-175 (2011)
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hisat2
??? missing short description for package hisat2 :-(
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hmmer
??? missing short description for package hmmer :-(
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Please cite: S. R. Eddy: Profile hidden Markov models. (PubMed,eprint) Bioinformatics 14(9):755-763 (1998)
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idba
??? missing short description for package idba :-(
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Please cite: Yu Peng, Henry C. M. Leung, S. M. Yiu and Francis Y. L. Chin: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. (PubMed,eprint) Bioinformatics 28(11):1420-1428 (2012)
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infernal
??? missing short description for package infernal :-(
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Please cite: Eric P. Nawrocki, Diana L. Kolbe and Sean R. Eddy: Infernal 1.0: inference of RNA alignments. (PubMed,eprint) Bioinformatics 25(10):1335-1337 (2009)
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jellyfish
??? missing short description for package jellyfish :-(
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Please cite: Guillaume Marcais and Carl Kingsford: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764-770 (2011)
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kalign
??? missing short description for package kalign :-(
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Please cite: Lassmann, Timo.: Kalign 3: multiple sequence alignment of large datasets. (eprint) Bioinformatics 36(6):1928-1929 (2020)
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kissplice
??? missing short description for package kissplice :-(
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Please cite: Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix: KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. (PubMed,eprint) BMC Bioinformatics 13((Suppl 6)):S5 (2012)
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Topics: RNA-seq; RNA splicing; Gene structure
last-align
??? missing short description for package last-align :-(
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Please cite: Martin C. Frith, Raymond Wan and Paul Horton: Incorporating sequence quality data into alignment improves DNA read mapping. (PubMed,eprint) Nucl. Acids Res. 38(7):e100 (2010)
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loki
??? missing short description for package loki :-(
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The package is enhanced by the following packages: loki-doc
macs
??? missing short description for package macs :-(
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Please cite: Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S. Johnson, Bradley E. Bernstein, Chad Nussbaum, Richard M. Myers, Myles Brown, Wei Li and X Shirley Liu: Model-based Analysis of ChIP-Seq (MACS). (PubMed,eprint) Genome Biol. 9(9):R137 (2008)
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mafft
??? missing short description for package mafft :-(
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Please cite: Kazutaka Katoh and Hiroyuki Toh: Recent developments in the MAFFT multiple sequence alignment program. (PubMed) Brief Bioinform 9(4):286-298 (2008)
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mapsembler2
??? missing short description for package mapsembler2 :-(
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Please cite: Pierre Peterlongo and Rayan Chikhi: Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. (PubMed) BMC Bioinformatics 13:48 (2012)
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maq
??? missing short description for package maq :-(
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Please cite: Heng Li, Jue Ruan and Richard Durbin: Mapping short DNA sequencing reads and calling variants using mapping quality scores. (PubMed,eprint) Genome Research 18(11):1851-1858 (2008)
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melting
??? missing short description for package melting :-(
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Please cite: Le Novère, Nicolas: MELTING, computing the melting temperature of nucleic acid duplex. (PubMed,eprint) Bioinformatics 17(12):1226-1227 (2001)
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minia
??? missing short description for package minia :-(
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Please cite: Rayan Chikhi and Guillaume Rizk: Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter.. (PubMed,eprint) Algorithms for Molecular Biology 8(1):22 (2013)
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Topics: Sequence assembly
mipe
??? missing short description for package mipe :-(
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Please cite: Jan Aerts and T. Veenendaal: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data. Online Journal of Bioinformatics 6(2):114-120 (2005)
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mira-assembler
??? missing short description for package mira-assembler :-(
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Please cite: Bastien Chevreux, Thomas Pfisterer, Bernd Drescher, Albert J. Driesel, Werner E. G. Müller, Thomas Wetter and Sándor Suhai: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. (PubMed,eprint) Genome Research 14(6):1147-1159 (2004)
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mlv-smile
??? missing short description for package mlv-smile :-(
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Please cite: L. Marsan and M.-F. Sagot: Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification. (PubMed,eprint) J. of Comput. Biol. 7(3-4):345-362 (2000)
mothur
??? missing short description for package mothur :-(
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Please cite: Patrick D Schloss, Sarah L Westcott, Thomas Ryabin, Justine R Hall, Martin Hartmann, Emily B Hollister, Ryan A Lesniewski, Brian B Oakley, Donovan H Parks, Courtney J Robinson, Jason W Sahl, Blaz Stres, Gerhard G Thallinger, David J Van Horn and Carolyn F Weber: Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. (PubMed) Appl Environ Microbiol 75(23):7537-7541 (2009)
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Topics: Microbial ecology
mrbayes
??? missing short description for package mrbayes :-(
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The package is enhanced by the following packages: mrbayes-doc
Please cite: Fredrik Ronquist, Maxim Teslenko, Paul van der Mark, Daniel L. Ayres, Aaron Darling, Sebastian Höhna, Bret Larget, Liang Liu, Marc A. Suchard and John P. Huelsenbeck: MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. (PubMed,eprint) Systematic Biology (2012)
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mummer
??? missing short description for package mummer :-(
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The package is enhanced by the following packages: e-mem
Please cite: Stefan Kurtz, Adam Phillippy, Arthur L. Delcher, Michael Smoot, Martin Shumway, Corina Antonescu and Steven L. Salzberg: Versatile and open software for comparing large genomes. (PubMed) Genome Biology 5(2):R12 (2004)
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muscle
??? missing short description for package muscle :-(
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Please cite: Robert C. Edgar: MUSCLE: multiple sequence alignment with high accuracy and high throughput. (PubMed,eprint) Nucleic Acids Research 32(5):1792-1797 (2004)
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muscle3
??? missing short description for package muscle3 :-(
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Please cite: Robert C. Edgar: MUSCLE: multiple sequence alignment with high accuracy and high throughput. (PubMed,eprint) Nucleic Acids Research 32(5):1792-1797 (2004)
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Topics: Sequence analysis
mustang
??? missing short description for package mustang :-(
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The package is enhanced by the following packages: mustang-testdata
Please cite: Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey and Arthur M. Lesk: MUSTANG: A multiple structural alignment algorithm. (PubMed) Proteins: Structure, Function, and Bioinformatics 64(3):559-574 (2006)
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ncbi-epcr
??? missing short description for package ncbi-epcr :-(
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Please cite: Gregory D. Schuler: Sequence Mapping by Electronic PCR. (PubMed,eprint) Genome Research 7(5):541-550 (1997)
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ncbi-tools-bin
??? missing short description for package ncbi-tools-bin :-(
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The package is enhanced by the following packages: mcl
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ncoils
??? missing short description for package ncoils :-(
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Please cite: Andrei Lupas, Marc Van Dyke and Jeff Stock: Predicting coiled coils from protein sequences. (PubMed) Science 252:1162-1164 (1991)
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neobio
??? missing short description for package neobio :-(
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Please cite: Maxime Crochemore, Gad M. Landau and Michal Ziv-Ukelson: A sub-quadratic sequence alignment algorithm for unrestricted cost matrices. :679-688 (2002)
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paraclu
??? missing short description for package paraclu :-(
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Please cite: Martin C. Frith, Eivind Valen, Anders Krogh, Yoshihide Hayashizaki, Piero Carninci and Albin Sandelin: A code for transcription initiation in mammalian genomes. (eprint) Genome Research 18(1):1-12 (2008)
parsinsert
??? missing short description for package parsinsert :-(
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The package is enhanced by the following packages: parsinsert-testdata
pdb2pqr
??? missing short description for package pdb2pqr :-(
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Please cite: Todd J Dolinsky, Paul Czodrowski, Hui Li, Jens E Nielsen, Jan H Jensen, Gerhard Klebe and Nathan A Baker: PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. (PubMed,eprint) Nucleic Acids Research 35:W522-5 (2007)
perm
??? missing short description for package perm :-(
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Please cite: Yangho Chen, Tade Souaiaia and Ting Chen: PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. (PubMed,eprint) Bioinformatics 25(19):2514-21 (2009)
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phyml
??? missing short description for package phyml :-(
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Please cite: Stéphane Guindon: Bayesian estimation of divergence times from large sequence alignments. (PubMed,eprint) Molecular Biology and Evolution 27(8):1768-81 (2010)
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phyutility
??? missing short description for package phyutility :-(
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Please cite: Stephen A. Smith and Casey W. Dunn: Phyutility: a phyloinformatics utility for trees, alignments, and molecular data. (PubMed,eprint) Bioinformatics 24(5):715-716 (2008)
picard-tools
??? missing short description for package picard-tools :-(
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The package is enhanced by the following packages: multiqc
Please cite: Broad Institute: Picard toolkit. Broad Institute, GitHub repository (2019)
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Topics: Sequencing; Document, record and content management
plink
??? missing short description for package plink :-(
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Please cite: Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A. R. Ferreira, David Bender, Julian Maller, Pamela Sklar, Paul I. W. de Bakker, Mark J. Daly and Pak C. Sham: PLINK: a toolset for whole-genome association and population-based linkage analysis. (PubMed) American Journal of Human Genetics 81(3):559-75 (2007)
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plink1.9
??? missing short description for package plink1.9 :-(
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Please cite: Christopher C. Chang, Carson C. Chow, Laurent C.A.M. Tellier, Shashaank Vattikuti, Shaun M. Purcell and James J. Lee: Second-generation PLINK: rising to the challenge of larger and richer datasets. (eprint) GigaScience 4(1):7 (2015)
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plink2
??? missing short description for package plink2 :-(
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Please cite: Christopher C. Chang, Carson C. Chow, Laurent C.A.M. Tellier, Shashaank Vattikuti, Shaun M. Purcell and James J. Lee: Second-generation PLINK: rising to the challenge of larger and richer datasets. (eprint) GigaScience 4(1):7 (2015)
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poa
??? missing short description for package poa :-(
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Please cite: Catherine Grasso and Christopher Lee: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. (PubMed) Bioinformatics 20(10):1546-1556 (2004)
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prank
??? missing short description for package prank :-(
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Please cite: Ari Löztznoja: Phylogeny-aware alignment with PRANK. (PubMed) Methods Mol. Biol. 1079:155-170 (2014)
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prime-phylo
??? missing short description for package prime-phylo :-(
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Please cite: Ö. Åkerborg, B. Sennblad, L. Arvestad and J. Lagergren: Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. (PubMed,eprint) Proceedings of the National Academy of Sciences 106(14):5714-5719 (2009)
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primer3
??? missing short description for package primer3 :-(
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Please cite: Steve Rozen and Helen J. Skaletsky: Primer3 on the WWW for general users and for biologist programmers. (PubMed,eprint) Methods Mol Biol. 132(3):365-86 (2000)
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probabel
??? missing short description for package probabel :-(
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The package is enhanced by the following packages: probabel-examples
Please cite: Yurii S Aulchenko, Maksim V Struchalin and Cornelia M van Duijn: ProbABEL package for genome-wide association analysis of imputed data.. (PubMed,eprint) BMC Bioinformatics 11:134 (2010)
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probcons
??? missing short description for package probcons :-(
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Please cite: Chuong B. Do, Mahathi S.P. Mahabhashyam, Michael Brudno and Serafim Batzoglou: ProbCons: Probabilistic consistency-based multiple sequence alignment. (PubMed,eprint) Genome Research 15(2):330-340 (2005)
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proda
??? missing short description for package proda :-(
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Please cite: Tu Minh Phuong, Chuong B. Do, Robert C. Edgar and Serafim Batzoglou: Multiple alignment of protein sequences with repeats and rearrangements. (PubMed,eprint) Nucl. Acids Res. 34(20):5932-5942 (2006)
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prodigal
??? missing short description for package prodigal :-(
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Please cite: Doug Hyatt, Gwo-Liang Chen, Philip F. Locascio, Miriam L. Land, Frank W. Larimer and Loren J. Hauser: Prodigal: prokaryotic gene recognition and translation initiation site identification. (PubMed,eprint) BMC Bioinformatics 11:119 (2010)
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python3-biomaj3-cli
??? missing short description for package python3-biomaj3-cli :-(
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python3-biopython
??? missing short description for package python3-biopython :-(
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Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
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python3-cogent3
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Please cite: Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying and Gavin A Huttley: PyCogent: a toolkit for making sense from sequence. (PubMed,eprint) Genome Biology 8(8):R171 (2007)
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qiime
??? missing short description for package qiime :-(
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Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (PubMed,eprint) Nature Biotechnology 37:852 - 857 (2019)
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Topics: Microbial ecology
r-bioc-edger
??? missing short description for package r-bioc-edger :-(
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Please cite: Mark D. Robinson, Davis J. McCarthy and Gordon K. Smyth: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. (PubMed,eprint) Bioinformatics 26,:139-140 (2010)
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r-bioc-hilbertvis
??? missing short description for package r-bioc-hilbertvis :-(
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Please cite: Simon Anders: Visualization of genomic data with the Hilbert curve. (PubMed,eprint) Bioinformatics 25(10):1231-1235 (2009)
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r-cran-pvclust
??? missing short description for package r-cran-pvclust :-(
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Please cite: Ryota Suzuki and Hidetoshi Shimodaira: Pvclust: an R package for assessing the uncertainty in hierarchical clustering. (PubMed,eprint) Bioinformatics 22(12):1540-1542 (2006)
r-cran-qtl
??? missing short description for package r-cran-qtl :-(
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Please cite: Karl W. Broman, Hao Wu, Saunak Sen and Gary A. Churchill: R/qtl: QTL mapping in experimental crosses. (PubMed,eprint) Bioinformatics 19:889-890 (2003)
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r-cran-vegan
??? missing short description for package r-cran-vegan :-(
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r-other-mott-happy.hbrem
??? missing short description for package r-other-mott-happy.hbrem :-(
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Please cite: Richard Mott, Christopher J. Talbot, Maria G. Turri, Allan C. Collins and Jonathan Flint: A method for fine mapping quantitative trait loci in outbred animal stocks. (PubMed,eprint) Proc. Natl. Acad. Sci. USA 97(23):12649-12654 (2000)
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raster3d
??? missing short description for package raster3d :-(
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Please cite: E.A. Merritt and D.J. Bacon: Raster3D Photorealistic Molecular Graphics. (PubMed) Methods in Enzymology 277:505-524 (1997)
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readseq
??? missing short description for package readseq :-(
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Please cite: Don Gilbert: Sequence file format conversion with command-line readseq. (PubMed,eprint) Current Protocols in Bioinformatics Appendix 1:E (2003)
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rnahybrid
??? missing short description for package rnahybrid :-(
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Please cite: Marc Rehmsmeier, Peter Steffen, Matthias Höchsmann and Robert Giegerich: Fast and effective prediction of microRNA/target duplexes. (PubMed,eprint) RNA 10(10):1507-1517 (2004)
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rtax
??? missing short description for package rtax :-(
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Please cite: David A. W. Soergel, Neelendu Dey, Rob Knight and Steven E. Brenner: Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. (PubMed,eprint) The ISME Journal 6:1440–1444 (2012)
samtools
??? missing short description for package samtools :-(
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The package is enhanced by the following packages: libbio-samtools-perl multiqc
Please cite: Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin and 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map (SAM) Format and SAMtools. (PubMed,eprint) Bioinformatics 25(16):2078-2079 (2009)
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seqan-apps
??? missing short description for package seqan-apps :-(
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Please cite: Andreas Doring, David Weese, Tobias Rausch and Knut Reinert: SeqAn An efficient, generic C++ library for sequence analysis. (PubMed,eprint) BMC Bioinformatics 9(1):11 (2008)
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sibsim4
??? missing short description for package sibsim4 :-(
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sigma-align
??? missing short description for package sigma-align :-(
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Please cite: Siddharthan, Rahul: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. (PubMed) BMC Bioinformatics 7(1):143 (2006)
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sim4
??? missing short description for package sim4 :-(
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Please cite: Liliana Florea, George Hartzell, Zheng Zhang, Gerald M. Rubin and Webb Miller: A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence. (PubMed,eprint) Genome Research 8:967-974 (1998)
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smalt
??? missing short description for package smalt :-(
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snap
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Please cite: Ian Korf: Gene finding in novel Genomes. (PubMed,eprint) BMC Bioinformatics 5:59 (2004)
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soapdenovo
??? missing short description for package soapdenovo :-(
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Please cite: Ruiqiang Li, Hongmei Zhu, Jue Ruan, Wubin Qian, Xiaodong Fang, Zhongbin Shi, Yingrui Li, Shengting Li, Gao Shan, Karsten Kristiansen, Songgang Li, Huanming Yang, Jian Wang and Jun Wang: De novo assembly of human genomes with massively parallel short read sequencing. (PubMed,eprint) Genome Research 20(2):265-72 (2009)
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soapdenovo2
??? missing short description for package soapdenovo2 :-(
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Please cite: Ruibang Luo, Binghang Liu, Yinlong Xie, Zhenyu Li, Weihua Huang, Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu, Jingbo Tang, Gengxiong Wu, Hao Zhang, Yujian Shi, Yong Liu, Chang Yu, Bo Wang, Yao Lu, Changlei Han, David W Cheung, Siu-Ming Yiu, Shaoliang Peng, Zhu Xiaoqian, Guangming Liu, Xiangke Liao, Yingrui Li, Huanming Yang, Jian Wang, Tak-Wah Lam and Jun Wang: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Giga Science 1(1):18 (2012)
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sra-toolkit
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ssake
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Please cite: Rene L. Warren, Granger G. Sutton, Steven J. M. Jones and Robert A. Holt: Assembling millions of short DNA sequences using SSAKE. (PubMed,eprint) Bioinformatics 23(4):500-501 (2007)
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staden-io-lib-utils
??? missing short description for package staden-io-lib-utils :-(
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t-coffee
??? missing short description for package t-coffee :-(
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The package is enhanced by the following packages: clustalw dialign-tx kalign mafft muscle muscle3 ncbi-blast+ poa prank probcons tm-align
Please cite: Cédric Notredame, Desmond G. Higgins and Jaap Heringa: T-coffee: a novel method for fast and accurate multiple sequence alignment. (PubMed) Journal of Molecular Biology 302(1):205-217 (2000)
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tabix
??? missing short description for package tabix :-(
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Please cite: Heng Li: Tabix: fast retrieval of sequence features from generic TAB-delimited files. (PubMed,eprint) Bioinformatics 27(5):718-719 (2011)
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theseus
??? missing short description for package theseus :-(
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The package is enhanced by the following packages: theseus-examples
Please cite: Douglas L. Theobald and Deborah S. Wuttke: THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. (eprint) Bioinformatics 22(17):2171-2172 (2006)
tigr-glimmer
??? missing short description for package tigr-glimmer :-(
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Please cite: Steven L. Salzberg, Arthur L. Delcher, S. Kasif and O. White: Microbial gene identification using interpolated Markov models. (PubMed,eprint) Nucleic Acids Research 26(2):544-8 (1998)
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tree-ppuzzle
??? missing short description for package tree-ppuzzle :-(
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Please cite: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron and Arndt von Haeseler: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. (PubMed,eprint) Bioinformatics 18(3):502-504 (2002)
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tree-puzzle
??? missing short description for package tree-puzzle :-(
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Please cite: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron and Arndt von Haeseler: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. (PubMed,eprint) Bioinformatics 18(3):502-504 (2002)
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vcftools
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The package is enhanced by the following packages: multiqc
Please cite: Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean and Richard Durbin: The variant call format and VCFtools. (PubMed,eprint) Bioinformatics 27(15):2156-8 (2011)
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velvet
??? missing short description for package velvet :-(
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Please cite: Daniel R. Zerbino and Ewan Birney: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. (PubMed,eprint) Genome Research 18(5):821-829 (2008)
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veryfasttree
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wise
??? missing short description for package wise :-(
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Please cite: Ewan Birney, Michele Clamp and Richard Durbin: GeneWise and Genomewise. (PubMed,eprint) Genome Research 14(5):988-95 (2004)
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Debian packages in contrib or non-free

cufflinks
??? missing short description for package cufflinks :-(
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Please cite: Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold and Lior Pachter: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. (PubMed) Nature Biotechnology 28(5):511-515 (2010)
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Packaging has started and developers might try the packaging code in VCS

bagpipe
genomewide LD mapping
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Bagpipe is a program for performing genomewide linkage disequilibrium mapping of quantitative trait loci in populations whose genome structure can be accommodated in the HAPPY framework [Mott00]. This includes most diploid crosses where the founders of the individuals have known genotypes.

  • Bagpipe is a simplified and streamlined version of Bagphenotype that does not currently include resample model averaging (RMA) capabilities.
  • Bagpipe can help fit single locus regression models (with or without random effects) to marker intervals whose genetic ancestry is inferred using the HAPPY software.
  • Bagpipe cannot help you decide what is a sensible model to fit.
  • Bagpipe does not currently accommodate populations with significant population structure, except through the specification of simple random intercepts based on unpatterned covariance matrices.
  • Bagpipe is named after the Scottish wind instrument "the bagpipes" and after Bagphenotype, which in turn was a PIPEline for BAGging-based multiple QTL analysis of phenoTYPEs. Bagphenotype was in turn based on software written by Richard Mott and William Valdar to analyze heterogeneous stock mice in [Valdar06].
  • Bagpipe is experimental software, is provided free of charge subject to copyleft restrictions, and comes with no guarantees whatsoever.
Please cite: Richard Mott, Christopher J. Talbot, Maria G. Turri, Allan C. Collins and Jonathan Flint: A method for fine mapping quantitative trait loci in outbred animal stocks. (PubMed) Proc Natl Acad Sci U S A. 97(23):12649-54 (200)
embassy-phylip
EMBOSS conversions of the programs in the phylip package
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This package is the adaptation of the PHYLIP package in which its programs can operate with the biological sequence formats and databases of the European Molecular Biology Open Software Suite (EMBOSS). The software packages adapted for EMBOSS are called EMBASSY.

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.

The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them from the original programs and avoid namespace conflict.
giira
RNA-Seq driven gene finding incorporating ambiguous reads
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GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment. It was foremost designed for prokaryotic gene prediction and is able to resolve genes within the expressed region of an operon. However, it is also applicable to eukaryotes and predicts exon intron structures as well as alternative isoforms.
Please cite: Franziska Zickmann, Martin S. Lindner and Bernhard Y. Renard: GIIRA—RNA-Seq driven gene finding incorporating ambiguous reads. (PubMed,eprint) Bioinformatics (2013)
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